annotate pepquery2_show_sets.xml @ 2:d39a43a076fc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f
author galaxyp
date Wed, 08 May 2024 17:12:13 +0000
parents b9e1e95758e8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
1 <tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
2 <description>PepQueryDB datasets, Parameters, PTMs</description>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
3 <macros>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
4 <import>macros.xml</import>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
5 </macros>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
6 <requirements>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
8 </requirements>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
10 echo "PepQuery2 Show Sets $sets"
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
11 #if 'PepQueryDB_datasets' in $sets
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
12 && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g' > '$pepquerydb'
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
13 #end if
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
14 #if 'parameter_sets' in $sets
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
15 && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
16 #end if
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
17 #if 'printPTM' in $sets
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
18 && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
19 #end if
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
20 ]]></command>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
21 <inputs>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
22 <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
23 <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
24 <option value="parameter_sets">PepQuery Predefined Parameter Sets</option>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
25 <option value="printPTM">PepQuery Modifications</option>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
26 </param>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
27 </inputs>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
28 <outputs>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
29 <data name="pepquerydb" format="tabular" label="PepQueryDB datasets">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
30 <filter>'PepQueryDB_datasets' in sets</filter>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
31 <actions>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
32 <action name="comment_lines" type="metadata" default="1" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
33 <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
34 </actions>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
35 </data>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
36 <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
37 <filter>'parameter_sets' in sets</filter>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
38 </data>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
39 <data name="ptm_list" format="tabular" label="PepQuery Modifications">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
40 <filter>'printPTM' in sets</filter>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
41 <actions>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
42 <action name="comment_lines" type="metadata" default="1" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
43 <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
44 </actions>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
45 </data>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
46 </outputs>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
47 <tests>
2
d39a43a076fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f
galaxyp
parents: 0
diff changeset
48 <test expect_num_outputs="1">
0
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
49 <output name="pepquerydb">
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
50 <assert_contents>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
51 <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
52 </assert_contents>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
53 </output>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
54 </test>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
55 </tests>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
56 <help><![CDATA[
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
57 **Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)*
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
58
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
59 @PEPQUERY_DOCUMANTATION_URL@
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
60
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
61 **PepQueryDB Datasets**
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
62
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
63 - Shows a table of all the indexed MS/MS datasets available in PepQueryDB.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
64 - *java -jar pepquery-2.0.2.jar -b show_full*
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
65 - These datasets can be used for the **-b** option in **PepQuery**.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
66 - The parameter_set value can be used in the **-p** option in **PepQuery**.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
67 - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
68
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
69
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
70 **PepQuery Predefined Parameter Sets**
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
71
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
72 - Shows the predefined Parameter Set Names with the option settings
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
73 - *java -jar pepquery-2.0.2.jar -p show*
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
74 - The parameterset names can be used for the **-p** option in **PepQuery**.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
75
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
76
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
77 **PepQuery Modifications**
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
78
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
79 - Shows a table of the PTMs available
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
80 - *java -jar pepquery-2.0.2.jar -printPTM*
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
81 - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
82 - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
83
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
84 ]]></help>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
85 <expand macro="citations" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
86 </tool>